Weird Issue

So my Nexus 7 is rooted and has been running an AOSP 4.4 rom. I am looking to upgrade my rom however when I go to update my clockworkmod it gives me an error message. When I go into Super User it says I am not rooted. What do I do at this point? Im at a complete loss.

XDA Developers was founded by developers, for developers. It is now a valuable resource for people who want to make the most of their mobile devices, from customizing the look and feel to adding new functionality.Are you a developer? | Terms of Service